MERFISH Report
1. Overview
Principle Investigator: Mehrdad Shamloo
Institution: Stanford
Project: SPR22-003 Aged Sleep Deprivation study
1.1 Slice Submission
This is the detailed slice information we got from collaborators:
| Sample ID | Anatomical source | Preparation method | Treatments | Species & Genetic background | Sex | Age |
|---|---|---|---|---|---|---|
| 1 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 18 months | mouse c57bl6 | m | 18 mo |
| 2 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 18 months | mouse c57bl7 | m | 18 mo |
| 3 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 18 months | mouse c57bl8 | m | 18 mo |
| 23 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 18 months | mouse c57bl9 | m | 18 mo |
| 24 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 18 months | mouse c57bl10 | m | 18 mo |
| 25 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 18 months | mouse c57bl11 | m | 18 mo |
| 31 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl12 | m | 4 mo |
| 32 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl13 | m | 4 mo |
| 33 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl14 | m | 4 mo |
| 34 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl15 | m | 4 mo |
| 35 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl16 | m | 4 mo |
| 36 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl17 | m | 4 mo |
| 37 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl18 | m | 4 mo |
| 38 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl19 | m | 4 mo |
| 39 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl20 | m | 4 mo |
| 40 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl21 | m | 4 mo |
1.2 Sample Information
A brief sample information is generated from the submission table for the following analysis.
“SD” refers to “Sleep Deprivation” while “nSD” refers to “No Sleep Deprivation”.
| Batch | Index | Genotype | region | Mice Age (month) | Data Path |
|---|---|---|---|---|---|
| 1 | nSD1 | nSD | region_0 | 18 | 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101 |
| 1 | SD23 | SD | region_1 | 18 | 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101 |
| 2 | nSD2 | nSD | region_0 | 18 | 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201 |
| 2 | SD24 | SD | region_1 | 18 | 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201 |
| 3 | nSD3 | nSD | region_0 | 18 | 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201 |
| 3 | SD25 | SD | region_1 | 18 | 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201 |
| 4 | SD36 | SD | region_0 | 4 | 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101 |
| 4 | nSD31 | nSD | region_1 | 4 | 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101 |
| 5 | SD37 | SD | region_0 | 4 | 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101 |
| 5 | nSD32 | nSD | region_1 | 4 | 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101 |
| 6 | SD38 | SD | region_0 | 4 | 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201 |
| 6 | nSD33 | nSD | region_1 | 4 | 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201 |
1.3 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Generally, log10 transcript count > 5.0 in most area can be considered as a good quality standard.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary